Running the Right Version of BionetSolver with CC3D

I’ve recently completed a second version of BionetSolver that I’ve called BionetSolver 1.0.0. It’s a fair amount faster than version 0.0.6, although the speedup scales with the number of bionetworks. If your CC3D-BionetSolver simulation only has a single bionetwork, then there won’t be much speed difference between 0.0.6 and 1.0.0. However, if you have 20, 40, 100 or more bionetworks, there will be noticeable (and pretty significant) speedup.

All that said, though, I wanted to write this post to clarify something about running the correct versions of BionetSolver with the correct versions of CC3D. Let me just list out some important points:

BionetSolver must be used with CC3D 3.5.0 or newer. Right now, the newest version of CC3D is 3.6.0.

CC3D 3.5.0 uses Python 2.5 while CC3D 3.6.0 uses Python 2.7. BionetSolver needs to be linked to the appropriate version of Python to be used with CC3D.

Either BionetSolver 0.0.6 or 1.0.0 may be used with CC3D 3.5.0 and 3.6.0 as long as it is linked to the correct version of Python.

So, I have built four versions of BionetSolver. I have a version of BionetSolver 0.0.6 linked to Python 2.5 and another version linked to Python 2.7. Likewise, I have a version of BionetSolver 1.0.0 linked to Python 2.5 and another version linked to Python 2.5.

And lastly, it’s important to note that there have been some minor changes to the BionetSolver API with version 1.0.0. If you look in the \Demos\BionetSolverExamples folder after installing BionetSolver 1.0.0, you’ll see two Word documents. One is a quick start guide for BionetSolver 0.0.6 and the other is a document describing version 1.0.0 (particularly describing the minor API changes with respect to version 0.0.6). The basic information in the BionetSolver 0.0.6 quick start guide is essentially the same for version 1.0.0 except for the minor API changes. The bionetAPI function names are almost exactly the same as for version 0.0.6 but the arguments for a few of these functions are slightly different in version 1.0.0. So take a look at both of these documents. *And* of course look at the demos in the \Demos\BionetSolverExamples folder. All Demos have been appropriately revised for version 1.0.0 so that these demos will be a good resource for learning the slight differences between the 0.0.6 API and the version 1.0.0 API.